-
1
-
-
77950142931
-
A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements
-
ALEMANI, D., COLLU, F., CASCELLA, M. & DAL PERARO, M. (2010). A nonradial coarse-grained potential for proteins produces naturally stable secondary structure elements. J. Chem. Theor. Comput. 6, 315-324.
-
(2010)
J. Chem. Theor. Comput.
, vol.6
, pp. 315-324
-
-
Alemani, D.1
Collu, F.2
Cascella, M.3
Dal Peraro, M.4
-
2
-
-
79951672258
-
Multi-scale modeling molecular dynamics of the Artichoke Mottled
-
in preparation in preparation
-
ARCANGELI, C. & TOZZINI, V. (in preparation). Multi-scale modeling molecular dynamics of the Artichoke Mottled. Crinkle Virus, in preparation.
-
Crinkle Virus
-
-
Arcangeli, C.1
Tozzini, V.2
-
3
-
-
0000550720
-
Strength of hydrogen bonds in alpha helices
-
ARORA, N. & JAYARAM, B. (1996). Strength of hydrogen bonds in alpha helices. J. Comput. Chem. 18, 1246-1252.
-
(1996)
J. Comput. Chem.
, vol.18
, pp. 1246-1252
-
-
Arora, N.1
Jayaram, B.2
-
4
-
-
0035132230
-
Anisotropy of fluctuation dynamics of proteins with an elastic network model
-
ATILGAN, A. R., DURELL, S. R., JERNIGAN, R. L., DEMIREL, M. C., KESKIN, O. & BAHAR, I. (2001). Anisotropy of fluctuation dynamics of proteins with an elastic network model. Biophys. J. 80, 505-515.
-
(2001)
Biophys. J.
, vol.80
, pp. 505-515
-
-
Atilgan, A.R.1
Durell, S.R.2
Jernigan, R.L.3
Demirel, M.C.4
Keskin, O.5
Bahar, I.6
-
5
-
-
34247098754
-
Multiscale modeling of biomolecular systems: in serial and in parallel
-
DOI 10.1016/j.sbi.2007.03.004, PII S0959440X07000346, Theory and Simulation / Mecromolecular Assemblages
-
AYTON, G.S., NOID, W. G. & VOTH, G.A. (2007). Multiscale modeling of biomolecular systems: in serial and in parallel. Curr. Opin. Struct. Biol. 17, 192-198. (Pubitemid 46584804)
-
(2007)
Current Opinion in Structural Biology
, vol.17
, Issue.2
, pp. 192-198
-
-
Ayton, G.S.1
Noid, W.G.2
Voth, G.A.3
-
6
-
-
0031566950
-
Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
-
DOI 10.1006/jmbi.1996.0758
-
BAHAR, I. & JERNIGAN, R. L. (1997). Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J. Mol. Biol. 266, 195-214. (Pubitemid 27170528)
-
(1997)
Journal of Molecular Biology
, vol.266
, Issue.1
, pp. 195-214
-
-
Bahar, I.1
Jernigan, R.L.2
-
7
-
-
0030832809
-
Short-range conformational energies, secondary structure propensities, and recognition of correct sequence-structure matches
-
DOI 10.1002/(SICI)1097-0134(199711)29:3<292::AID-PROT4>3.0.CO;2-D
-
BAHAR, I., KAPLAN, M. & JERNIGAN, R.L. (1997). Short-range conformational energies, secondary structure propensities, and recognition of correct sequence- structure matches. Proteins 29, 292-308. (Pubitemid 27484221)
-
(1997)
Proteins: Structure, Function and Genetics
, vol.29
, Issue.3
, pp. 292-308
-
-
Bahar, I.1
Kaplan, M.2
Jernigan, R.L.3
-
8
-
-
0034112766
-
Solution structure of biopolymers: A new method of constructing a bead model
-
BANACHOWICZ, E., GAPINSKI, J. & PATKOWSKI, A. (2000). Solution structure of biopolymers: a new method of constructing a bead model. Biophys. J. 78, 70-78. (Pubitemid 30207119)
-
(2000)
Biophysical Journal
, vol.78
, Issue.1
, pp. 70-78
-
-
Banachowicz, E.1
Gapinski, J.2
Patkowski, A.3
-
9
-
-
0028226386
-
Hydrogen bond strength and beta-sheet propensities: The role of a side chain blocking effect
-
BAY, Y. & ENGLANDER, W. (1994). Hydrogen bond strength and beta-sheet propensities: the role of a side chain blocking effect. Proteins 18, 262-266.
-
(1994)
Proteins
, vol.18
, pp. 262-266
-
-
Bay, Y.1
Englander, W.2
-
10
-
-
0033005899
-
Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes
-
BETANCOURT, M. R. & THIRUMALAI, D. (1999). Pair potentials for protein folding: choice of reference states and sensitivity of predicted native states to variations in the interaction schemes. Protein Sci. 8, 361-369. (Pubitemid 29072436)
-
(1999)
Protein Science
, vol.8
, Issue.2
, pp. 361-369
-
-
Betancourt, M.R.1
Thirumalai, D.2
-
11
-
-
67650221686
-
Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field
-
BUCK, P. M. & BYSTROFF, C. (2009). Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field. Proteins 76, 331-342.
-
(2009)
Proteins
, vol.76
, pp. 331-342
-
-
Buck, P.M.1
Bystroff, C.2
-
12
-
-
77249089645
-
Challenges and perspectives in biomolecular simulations: From the atomistic picture to multiscale modeling
-
CASCELLA, M. & PERARO, M. D. (2008). Challenges and perspectives in biomolecular simulations: from the atomistic picture to multiscale modeling. Curr. Opin. Struct. Biol. 18, 630-640.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 630-640
-
-
Cascella, M.1
Peraro, M.D.2
-
13
-
-
33847126878
-
Binding pathways of ligands to HIV-1 Protease: Coarse-grained and atomistic simulations
-
DOI 10.1111/j.1747-0285.2007.00464.x
-
CHANG, C.-E., TRYLSKA, J., TOZZINI, V. & MCCAMMON, J. A. (2007). Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations. Chem. Biol. Drug Des. 69, 5-13. (Pubitemid 46277781)
-
(2007)
Chemical Biology and Drug Design
, vol.69
, Issue.1
, pp. 5-13
-
-
Chang, C.-E.A.1
Trylska, J.2
Tozzini, V.3
Andrew McCammon, J.4
-
14
-
-
25844440811
-
Elastic network models for understanding biomolecular machinery: From enzymes to supramolecular assemblies
-
DOI 10.1088/1478-3975/2/4/S12, PII S1478397505050612
-
CHENNUBHOTLA, C., RADER, A. J., LEE-WEI YANG, L.-W. & BAHAR, I. (2005). Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies. Phys. Biol. 2, S173-S180. (Pubitemid 41609444)
-
(2005)
Physical Biology
, vol.2
, Issue.4
-
-
Chennubhotla, C.1
Rader, A.J.2
Yang, L.-W.3
Bahar, I.4
-
15
-
-
0017868338
-
Empirical prediction of protein conformation
-
CHOU, P. Y. & FASMAN, G. D. (1978). Empirical prediction of protein conformation. Annu. Rev. Biochem. 47, 251-276.
-
(1978)
Annu. Rev. Biochem.
, vol.47
, pp. 251-276
-
-
Chou, P.Y.1
Fasman, G.D.2
-
16
-
-
36849057606
-
Coarse-grained free energy functions for studying protein conformational changes: A double-well network model
-
DOI 10.1529/biophysj.107.112060
-
CHU, J.-W. & VOTH, G. A. (2007). Coarse-grained free energy functions for studying protein conformational changes: a double-well network model. Biophys. J. 93, 3860-3871. (Pubitemid 350223804)
-
(2007)
Biophysical Journal
, vol.93
, Issue.11
, pp. 3860-3871
-
-
Chu, J.-W.1
Voth, G.A.2
-
17
-
-
0034685604
-
Topological and energetic factors: What determines the structural details of the transition state ensemble and 'en-route' intermediates for protein folding? An investigation for small globular proteins
-
CLEMENTI, C., NYMEYER, H. & ONUCHIC, J. N. (2000). Topological and energetic factors: what determines the structural details of the transition state ensemble and 'en-route' intermediates for protein folding? An investigation for small globular proteins. J. Mol. Biol. 298, 937-953.
-
(2000)
J. Mol. Biol.
, vol.298
, pp. 937-953
-
-
Clementi, C.1
Nymeyer, H.2
Onuchic, J.N.3
-
18
-
-
67651236198
-
The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation
-
DAS, A. & ANDERSEN, H. C. (2009). The multiscale coarse-graining method. III. A test of pairwise additivity of the coarse-grained potential and of new basis functions for the variational calculation. J. Chem. Phys. 131, 034102.
-
(2009)
J. Chem. Phys.
, vol.131
, pp. 034102
-
-
Das, A.1
Andersen, H.C.2
-
19
-
-
22544446147
-
Balancing energy and entropy: A minimalist model for the characterization of protein folding landscapes
-
DOI 10.1073/pnas.0409471102
-
DAS, P., MATYSIAK, S. & CLEMENTI, C. (2005). Balancing energy and entropy: a minimalist model for the characterization of protein folding landscapes. Proc. Natl. Acad. Sci. U.S.A. 102, 10141-10146. (Pubitemid 41023339)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.29
, pp. 10141-10146
-
-
Das, P.1
Matysiak, S.2
Clementi, C.3
-
20
-
-
12144268244
-
Protein interactions and fluctuations in a proteomic network using an elastic network model
-
DEMIREL, M. C. & KESKIN, O. (2005). Protein interactions and fluctuations in a proteomic network using an elastic network model. J. Biomol. Struct. Dyn. 22, 381-386. (Pubitemid 40105175)
-
(2005)
Journal of Biomolecular Structure and Dynamics
, vol.22
, Issue.4
, pp. 381-386
-
-
Demirel, M.C.1
Keskin, O.2
-
21
-
-
68149162202
-
Complexes of HIV-1 Integrase with HAT proteins: Multiscale models, dynamics and hypotheses on allos-teric sites of inhibition
-
DI FENZA, A., ROCCHIA, W. & TOZZINI, V. (2009). Complexes of HIV-1 Integrase with HAT proteins: multiscale models, dynamics and hypotheses on allos-teric sites of inhibition. Proteins 76, 946-958.
-
(2009)
Proteins
, vol.76
, pp. 946-958
-
-
Fenza A, D.I.1
Rocchia, W.2
Tozzini, V.3
-
22
-
-
84940492598
-
Interatomic potentials from first-principles calculations: The force-matching method
-
ERCOLESSI, F. & ADAMS, J. B. (1994). Interatomic potentials from first-principles calculations: the force-matching method. Europhys. Lett. 26, 583. (Pubitemid 24792682)
-
(1994)
Europhysics Letters
, vol.26
, Issue.8
, pp. 583
-
-
Ercolessi, F.1
Adams, J.B.2
-
23
-
-
33745024278
-
Symmetry, form, and shape: Guiding principles for robustness in macromolecular machines
-
FLORENCE TAMA, F. & BROOKS III, C. L. (2005). Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annu. Rev. Biophys. Biomol. Struct. 35, 115-133.
-
(2005)
Annu. Rev. Biophys. Biomol. Struct.
, vol.35
, pp. 115-133
-
-
Florence Tama, F.1
Brooks Iii, C.L.2
-
24
-
-
1942470951
-
Self-assembly of pep-tides into a b-barrel motif
-
FRIEDEL, M. & SHEA, J. M. (2004). Self-assembly of pep-tides into a b-barrel motif. J. Chem. Phys. 120, 5809.
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 5809
-
-
Friedel, M.1
Shea, J.M.2
-
25
-
-
0037799371
-
Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist b-barrel protein
-
FRIEDEL, M., SHEELER, D. J., & SHEA, J.-E. (2003). Effects of confinement and crowding on the thermodynamics and kinetics of folding of a minimalist b-barrel protein. J. Chem. Phys. 118, 8106-8113.
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 8106-8113
-
-
Friedel, M.1
Sheeler, D.J.2
Shea, J.-E.3
-
26
-
-
18344362394
-
On the use of classical statistical mechanics in the treatment of polymer chain conformation
-
GO, N. & SCHERAGA, H. A. (1976). On the use of classical statistical mechanics in the treatment of polymer chain conformation. Macromolecules 9, 535-542.
-
(1976)
Macromolecules
, vol.9
, pp. 535-542
-
-
N, G.O.1
Scheraga, H.A.2
-
27
-
-
77950114950
-
Protein backbone dynamics simulations using coarse-grained bonded potentials and simplified hydrogen bonds
-
HA-DUONG, T. (2010). Protein backbone dynamics simulations using coarse-grained bonded potentials and simplified hydrogen bonds. J. Chem. Theory Comput. 6, 761-773.
-
(2010)
J. Chem. Theory Comput.
, vol.6
, pp. 761-773
-
-
Ha-Duong, T.1
-
28
-
-
33846247964
-
Computing the amino acid specificity of fluctuations in biomolecular systems
-
HAMACHER, K. & MCCAMMON, J. A. (2006). Computing the amino acid specificity of fluctuations in biomolecular systems. J. Chem. Theory Comput. 2, 873-878.
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 873-878
-
-
Hamacher, K.1
McCammon, J.A.2
-
29
-
-
0025368288
-
Metastability of the folded states of globular proteins
-
HONEYCUTT, J. D. & THIRUMALAI, D. (1990). Metastability of the folded states of globular proteins. Proc. Natl. Acad. Sci. U.S.A. 87, 3526-3529.
-
(1990)
Proc. Natl. Acad. Sci. U.S.A.
, vol.87
, pp. 3526-3529
-
-
Honeycutt, J.D.1
Thirumalai, D.2
-
30
-
-
33748250745
-
Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers
-
IZVEKOV, S. & VOTH, G. A. (2006). Multiscale coarse-graining of mixed phospholipid/cholesterol bilayers. J. Chem. Theory Comput. 2, 637-648.
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 637-648
-
-
Izvekov, S.1
Voth, G.A.2
-
31
-
-
3042598406
-
Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: A new method for force-matching
-
IZVEKOV, S., PARRINELLO, M., BURNHAM, C.J. & VOTH, G. A. (2004). Effective force fields for condensed phase systems from ab initio molecular dynamics simulation: a new method for force-matching. J. Chem. Phys. 120, 10896-10913.
-
(2004)
J. Chem. Phys.
, vol.120
, pp. 10896-10913
-
-
Izvekov, S.1
Parrinello, M.2
Burnham, C.J.3
Voth, G.A.4
-
32
-
-
33644929350
-
Multiscale coarse graining of liquid-state systems
-
IZVEKOV, S. & VOTH, G. A. (2005). Multiscale coarse graining of liquid-state systems. J. Chem. Phys. 123, 134105.
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 134105
-
-
Izvekov, S.1
Voth, G.A.2
-
33
-
-
0346688724
-
Assembly and Kinetic Folding Pathways of A Tetrameric β-Sheet Complex: Molecular Dynamics Simulations on Simplified off-Lattice Protein Models
-
JANG, H., HALL, C. K. & ZHOU, Y. (2004). Assembly and kinetic folding pathways of a tetrameric b-sheet complex: molecular dynamics simulations on simplified off-lattice protein models. Biophys. J. 86, 31-49. (Pubitemid 38067434)
-
(2004)
Biophysical Journal
, vol.86
, Issue.1
, pp. 31-49
-
-
Jang, H.1
Hall, C.K.2
Zhou, Y.3
-
34
-
-
28944434207
-
A connection rule for α-carbon coarse-grained elastic network models using chemical bond information
-
DOI 10.1016/j.jmgm.2005.09.006, PII S1093326305001075
-
JEONG, J. I., JANG, Y. & KIM, M. K. (2005). A connection rule for a-carbon coarse-grained elastic network models using chemical bond information. J. Mol. Graph Model 24, 296-306. (Pubitemid 41786042)
-
(2006)
Journal of Molecular Graphics and Modelling
, vol.24
, Issue.4
, pp. 296-306
-
-
Jeong, J.I.1
Jang, Y.2
Kim, M.K.3
-
35
-
-
0037459035
-
Solvation effects and driving forces for protein thermodynamic and kinetic cooperativity: How adequate is native-centric topological modeling?
-
DOI 10.1016/S0022-2836(02)01434-1
-
KAYA, H. & CHAN, H. S. (2003). Solvation effects and driving forces for proteinthermodynamic and kinetic cooperativity: how adequate is native-centric topo-logical modeling? J. Mol. Biol. 326, 911-931. (Pubitemid 36279329)
-
(2003)
Journal of Molecular Biology
, vol.326
, Issue.3
, pp. 911-931
-
-
Kaya, H.1
Chan, H.S.2
-
36
-
-
0031678069
-
Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions
-
KESKIN, O., BAHAR, I., BADRETDINOV, A., PTITSYN, O. & JERNIGAN, R. (1998). Empirical solvent-mediated potentials hold for both intra-molecular and inter-molecular inter-residue interactions. Protein Sci. 7, 2578.
-
(1998)
Protein Sci.
, vol.7
, pp. 2578
-
-
Keskin, O.1
Bahar, I.2
Badretdinov, A.3
Ptitsyn, O.4
Jernigan, R.5
-
38
-
-
0032424129
-
Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: Effect on stability, cooperativity and kinetics
-
KLIMOV, D.K., BETANCOURT, M.R. & THIRUMALAI, D. (1998). Virtual atom representation of hydrogen bonds in minimal off-lattice models of alpha helices: effect on stability, cooperativity and kinetics. Folding Des. 3, 481-496.
-
(1998)
Folding Des.
, vol.3
, pp. 481-496
-
-
Klimov, D.K.1
Betancourt, M.R.2
Thirumalai, D.3
-
39
-
-
0035850732
-
Roles of native topology and chain-length scaling in protein folding: A simulation study with a g-like model
-
DOI 10.1006/jmbi.2001.5037
-
KOGA, N. & TAKADA, S. (2001). Roles of native topology and chain-length scaling in protein folding: a simulation study. J. Mol. Biol. 313, 171-180. (Pubitemid 33001173)
-
(2001)
Journal of Molecular Biology
, vol.313
, Issue.1
, pp. 171-180
-
-
Koga, N.1
Takada, S.2
-
40
-
-
70349458094
-
A force field for virtual atom molecular mechanics of proteins
-
KORKUTA, A. & HENDRICKSON, W. A. (2009). A force field for virtual atom molecular mechanics of proteins. Proc. Natl. Acad. Sci. U.S.A. 106, 15667-15672.
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 15667-15672
-
-
Korkuta, A.1
Hendrickson, W.A.2
-
41
-
-
10344230919
-
Automatic domain decomposition of proteins by a Gaussian Network Model
-
DOI 10.1002/prot.20268
-
KUNDU, S., SORENSEN, D. C., & PHILLIPS, JR., G. R. (2004). Automatic domain decomposition of proteins by a Gaussian network model. Proteins 57, 725-733. (Pubitemid 39626994)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.57
, Issue.4
, pp. 725-733
-
-
Kundu, S.1
Sorensen, D.C.2
Phillips Jr., G.N.3
-
42
-
-
0016610491
-
Computer simulation of protein folding
-
LEVITT, M. & WARSHEL, A. (1975). Computer simulation of protein folding. Nature 253, 694-698.
-
(1975)
Nature
, vol.253
, pp. 694-698
-
-
Levitt, M.1
Warshel, A.2
-
43
-
-
0017157584
-
A simplified representation of protein conformations for rapid simulation of protein folding
-
LEVITT, M. (1976). A simplified representation of protein conformations for rapid simulation of protein folding. J. Mol. Biol. 104, 59-107.
-
(1976)
J. Mol. Biol.
, vol.104
, pp. 59-107
-
-
Levitt, M.1
-
44
-
-
35348950936
-
Multi-scale coarse graining of monosaccharides
-
LIU, P., IZVEKOW, S. & VOTH, G. A. (2007). Multi-scale coarse graining of monosaccharides. J. Phys. Chem. B 111, 11566-11575.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 11566-11575
-
-
Liu, P.1
Izvekow, S.2
Voth, G.A.3
-
45
-
-
0000095892
-
A united-residue force field for off-lattice protein-structure simulations. I. Functional forms and parameters of long-range side-chain interaction potentials from protein crystal data
-
LIWO, A., OLDZIEJ, S., PINCUS, M.R., WAWAK, R.J., RACKOWSKY, S. & SCHERAGA, H. A. (1997a). A united-residue force field for off-lattice protein structure simulations. I. Functional forms and parameters of long range side chain interactions potentials from protein crystal data. J. Comput. Chem. 18, 849-873. (Pubitemid 127598574)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.7
, pp. 849-873
-
-
Liwo, A.1
Oldziej, S.2
Pincus, M.R.3
Wawak, R.J.4
Rackovsky, S.5
Scheraga, H.A.6
-
46
-
-
0000095890
-
A united-residue force field for off-lattice protein-structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by Z-score optimization
-
LIWO, A., PINCUS, M. R., WAWAK, R. J., RACKOWSKY, S., OLDZIEJ, S. & SCHERAGA, H. A. (1997b). A united-residue force field for off-lattice protein structure simulations. II. Parameterization of short-range interactions and determination of weights of energy terms by z-score optimization. J. Comput. Chem. 18, 874-887. (Pubitemid 127598575)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.7
, pp. 874-887
-
-
Liwo, A.1
Pincus, M.R.2
Wawak, R.J.3
Rackovsky, S.4
Oldziej, S.5
Scheraga, H.A.6
-
47
-
-
58149161251
-
Systematic multiscale parameterization of heterogeneous elastic network models of proteins
-
LYMAN, E., PFAENDTNER, J., & VOTH, G.A. (2008). Systematic multiscale parameterization of heterogeneous elastic network models of proteins. Biophys. J. 95, 4183-4192.
-
(2008)
Biophys. J.
, vol.95
, pp. 4183-4192
-
-
Lyman, E.1
Pfaendtner, J.2
Voth, G.A.3
-
48
-
-
68149165350
-
A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins
-
MÁJEK, P. & ELBER, R. (2009). A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins. Proteins 76, 822-836.
-
(2009)
Proteins
, vol.76
, pp. 822-836
-
-
Májek, P.1
Elber, R.2
-
49
-
-
24644483073
-
Large amplitude conformational change in proteins explored with a plastic network model: Adenylate kinase
-
DOI 10.1016/j.jmb.2005.07.031, PII S0022283605008193
-
MARAGAKIS, P. & KARPLUS, M. (2005). Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. J. Mol. Biol. 352, 807-822. (Pubitemid 41267070)
-
(2005)
Journal of Molecular Biology
, vol.352
, Issue.4
, pp. 807-822
-
-
Maragakis, P.1
Karplus, M.2
-
51
-
-
33748770940
-
Minimalist Protein Model as a Diagnostic Tool for Misfolding and Aggregation
-
DOI 10.1016/j.jmb.2006.07.088, PII S0022283606009879
-
MATYSIAK, S. & CLEMENTI, C. (2006). Minimalist protein model as a diagnostic tool for misfolding and aggregation. J. Mol. Biol. 363, 297-308. (Pubitemid 44414843)
-
(2006)
Journal of Molecular Biology
, vol.363
, Issue.1
, pp. 297-308
-
-
Matysiak, S.1
Clementi, C.2
-
52
-
-
84985740872
-
Helix-coil transition in a simple polypeptide model
-
MCCAMMON, J. A. & NORTHRUP, S. H. (1980). Helix-coil transition in a simple polypeptide model. Biopolymers 19, 2033-2045.
-
(1980)
Biopolymers
, vol.19
, pp. 2033-2045
-
-
McCammon, J.A.1
Northrup, S.H.2
-
53
-
-
0029919190
-
Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading
-
MIYAZAWA, S. & JERNIGAN, R. L. (1996). Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 256, 623.
-
(1996)
J. Mol. Biol.
, vol.256
, pp. 623
-
-
Miyazawa, S.1
Jernigan, R.L.2
-
54
-
-
49449113010
-
The MARTINI coarse-grained force field: Extension to proteins
-
MONTICELLI, L., KANDASAMY, S. K., PERIOLE, X., LARSON, R. G., TIELEMAN, D. P., & MARRINK, S.-J. (2008). The MARTINI coarse-grained force field: extension to proteins. J. Chem. Theory Comput. 4, 819-834.
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 819-834
-
-
Monticelli, L.1
Kandasamy, S.K.2
Periole, X.3
Larson, R.G.4
Tieleman, D.P.5
Marrink, S.-J.6
-
55
-
-
0037426218
-
Correlation between rate of folding, energy landscape and topology in the folding of a model protein HP-36
-
MUKHERJEE, A. & BAGCHI, B. (2002). Correlation between rate of folding, energy landscape and topology in the folding of a model protein HP-36. J. Chem. Phys. 118, 4733-4747.
-
(2002)
J. Chem. Phys.
, vol.118
, pp. 4733-4747
-
-
Mukherjee, A.1
Bagchi, B.2
-
56
-
-
34548064535
-
Orientation-dependent potential of mean force for protein folding
-
MUKHERJEE, A., BHIMALAPURAM, P. & BAGCHIA, B. (2005). Orientation-dependent potential of mean force for protein folding. J. Chem. Phys. 123, 014901.
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 014901
-
-
Mukherjee, A.1
Bhimalapuram, P.2
Bagchia, B.3
-
57
-
-
33750409944
-
Modeling protein thermodynamics and fluctuations at the mesoscale
-
NAKAGAWA, N. & PEYRARD, M. (2006). Modeling protein thermodynamics and fluctuations at the mesoscale. Phys. Rev. E 74, 041916.
-
(2006)
Phys. Rev. e
, vol.74
, pp. 041916
-
-
Nakagawa, N.1
Peyrard, M.2
-
58
-
-
46149109506
-
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
-
NOID, W. G., CHU, J.-W., AYTON, G. S., KRISHNA, V., IZVEKOV, S., VOTH, G. A., DAS, A. & ANDERSEN, H. C. (2008a). The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models. J Chem. Phys. 128, 244114.
-
(2008)
J Chem. Phys.
, vol.128
, pp. 244114
-
-
Noid, W.G.1
Chu, J.-W.2
Ayton, G.S.3
Krishna, V.4
Izvekov, S.5
Voth, G.A.6
Das, A.7
Andersen, H.C.8
-
59
-
-
46149099398
-
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
-
NOID, W. G., LIU, P., WANG, Y., CHU, J.-W., AYTON, G. S., IZVEKOV, S., ANDERSEN, H. C., & VOTH, G. A. (2008b). The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. J. Chem. Phys. 128, 244115.
-
(2008)
J. Chem. Phys.
, vol.128
, pp. 244115
-
-
Noid, W.G.1
Liu, P.2
Wang, Y.3
Chu, J.-W.4
Ayton, G.S.5
Izvekov, S.6
Andersen, H.C.7
Voth, G.A.8
-
60
-
-
0032568599
-
Folding funnels and frustration in off-lattice minimalist protein landscapes
-
DOI 10.1073/pnas.95.11.5921
-
NYMEYER, H., GARCIA, A. E. & ONUCHIC, J. N. (1998). Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc. Natl. Acad. Sci. U.S.A. 95, 5921-5928. (Pubitemid 28248940)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.11
, pp. 5921-5928
-
-
Nymeyer, H.1
Garcia, A.E.2
Onuchic, J.N.3
-
61
-
-
0037439922
-
Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins
-
OKUR, A., STROCKBINE, B., HORNAK, V. & SIMMERLING, C. (2003). Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. J. Comput. Chem. 24, 21-31.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 21-31
-
-
Okur, A.1
Strockbine, B.2
Hornak, V.3
Simmerling, C.4
-
62
-
-
0000626498
-
Peptide free-energy profile is strongly dependent on the force field: Comparison of C96 and AMBER95
-
ONO, S., NAKAJIMA, N., HIGO, J. & NAKAMURA, H. (2000). Peptide free-energy profile is strongly dependent on the force field: comparison of C96 and AMBER95. J. Comput. Chem. 21, 748-762.
-
(2000)
J. Comput. Chem.
, vol.21
, pp. 748-762
-
-
Ono, S.1
Nakajima, N.2
Higo, J.3
Nakamura, H.4
-
63
-
-
0042783950
-
Deriving effective mesoscale potentials from atomistic simulations
-
REITH, D., PÜTZ, M. & MÜLLER-PLATHE, F. (2003). Deriving effective mesoscale potentials from atomistic simulations. J. Comput. Chem. 24, 1624-1636.
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1624-1636
-
-
Reith, D.1
Pütz, M.2
Müller-Plathe, F.3
-
64
-
-
61349179602
-
The structural dynamics of macromolecular processes
-
RUSSELL, D., LASKER, K., PHILLIPS, J., SCHNEIDMAN-DUHOVNY, D., VELASZQUEZ-MURIEL, J.A. & SALI, A. (2009). The structural dynamics of macromolecular processes. Curr. Opin. Cell Biol. 21, 1-12.
-
(2009)
Curr. Opin. Cell Biol.
, vol.21
, pp. 1-12
-
-
Russell, D.1
Lasker, K.2
Phillips, J.3
Schneidman-Duhovny, D.4
Velaszquez-Muriel, J.A.5
Sali, A.6
-
65
-
-
53249098376
-
Multiscale methods for macromolecular simulations
-
SHERWOOD, P., BROOKS, B. R. & SANSOM, M. S. (2008). Multiscale methods for macromolecular simulations. Curr. Opin. Struct. Biol. 18, 630-640.
-
(2008)
Curr. Opin. Struct. Biol.
, vol.18
, pp. 630-640
-
-
Sherwood, P.1
Brooks, B.R.2
Sansom, M.S.3
-
66
-
-
33748266722
-
Mixed atomistic and coarse-grained molecular dynamics: Simulation of a membrane-bound ion channel
-
DOI 10.1021/jp062700h
-
SHI, Q., IZVEKOV, S., & VOTH, G. A. (2006). Mixed atomistic and coarse grained molecular dynamics: simulation of membrane a bound ion channel. J. Phys. Chem. B. 110, 15045-15048. (Pubitemid 44318467)
-
(2006)
Journal of Physical Chemistry B
, vol.110
, Issue.31
, pp. 15045-15048
-
-
Shi, Q.1
Izvekov, S.2
Voth, G.A.3
-
67
-
-
0032495778
-
A simple model of water and the hydrophobic effect
-
DOI 10.1021/ja973029k
-
SILVERSTEIN, K. A. T., HAYMET, A. D. J. & DILL, K. A. (1998). A simple model of water and the hydrophobic effect. J. Am. Chem. Soc. 120, 3166-3175. (Pubitemid 28204530)
-
(1998)
Journal of the American Chemical Society
, vol.120
, Issue.13
, pp. 3166-3175
-
-
Silverstein, K.A.T.1
Haymet, A.D.J.2
Dill, K.A.3
-
68
-
-
48949119100
-
Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors
-
SOHEILIFARD, R., MAKAROV, D. E. & RODIN, G. J. (2008). Critical evaluation of simple network models of protein dynamics and their comparison with crystallographic B-factors. Phys. Biol. 5, 026008.
-
(2008)
Phys. Biol.
, vol.5
, pp. 026008
-
-
Soheilifard, R.1
Makarov, D.E.2
Rodin, G.J.3
-
69
-
-
0036207492
-
Protein engineering study of protein L by simulation
-
DOI 10.1089/10665270252833181
-
SORENSON, J. M. & HEAD-GORDON, T. (2002a). Protein engineering study of protein L by simulation. J. Comput. Biol. 9, 35-54. (Pubitemid 34264285)
-
(2002)
Journal of Computational Biology
, vol.9
, Issue.1
, pp. 35-54
-
-
Sorenson, J.M.1
Head-Gordon, T.2
-
70
-
-
0036499417
-
Toward minimalist models of larger proteins: A ubiquitin-like protein
-
DOI 10.1002/prot.1174
-
SORENSON, J. M. & HEAD-GORDON, T. (2002b). Toward minimalist models of larger proteins: a ubiquitin-like protein. Proteins 46, 368-379. (Pubitemid 34184588)
-
(2002)
Proteins: Structure, Function and Genetics
, vol.46
, Issue.4
, pp. 368-379
-
-
Sorenson, J.M.1
Head-Gordon, T.2
-
71
-
-
55149087047
-
Peptide folding using multiscale coarse-grained models
-
THORPE, I. F., ZHOU, J. & VOTH, G. A. (2008). Peptide folding using multiscale coarse-grained models. J. Phys. Chem. B 112, 13079-13090.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 13079-13090
-
-
Thorpe, I.F.1
Zhou, J.2
Voth, G.A.3
-
72
-
-
0000197372
-
Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
-
TIRION, M. M. (1996). Large amplitude elastic motions in proteins from a single-parameter, atomic analysis. Phys. Rev. Lett. 77, 1905.
-
(1996)
Phys. Rev. Lett.
, vol.77
, pp. 1905
-
-
Tirion, M.M.1
-
73
-
-
17044393884
-
Coarse grained models for proteins
-
TOZZINI, V. (2005). Coarse grained models for proteins. Curr. Opin. Struct. Biol. 15, 144-150.
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
74
-
-
77249151455
-
Multi-scale modeling of proteins
-
TOZZINI, V. (2010). Multi-scale modeling of proteins. Acc. Chem. Res. 43, 220-230.
-
(2010)
Acc. Chem. Res.
, vol.43
, pp. 220-230
-
-
Tozzini, V.1
-
76
-
-
24344438610
-
A coarse grained model for the dynamics of flap opening in HIV-1 protease
-
DOI 10.1016/j.cplett.2005.07.075, PII S0009261405010663
-
TOZZINI, V. & MCCAMMON, J. A. (2005). A coarse grained model for the dynamics of flap opening in HIV-1 protease. Chem. Phys. Lett. 413, 123-128. (Pubitemid 41252378)
-
(2005)
Chemical Physics Letters
, vol.413
, Issue.1-3
, pp. 123-128
-
-
Tozzini, V.1
McCammon, J.A.2
-
78
-
-
33846213672
-
Mapping AA models onto one-bead coarse grained models: General properties and applications to a minimal polypeptide model
-
TOZZINI, V., ROCCHIA, W. & MCCAMMON, J. A. (2006). Mapping AA models onto one-bead coarse grained models: general properties and applications to a minimal polypeptide model. J. Chem. Theory Comput. 2, 667-673.
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 667-673
-
-
Tozzini, V.1
Rocchia, W.2
McCammon, J.A.3
-
79
-
-
33847116895
-
Flap opening dynamics in HIV-1 protease explored with a coarse-grained model
-
TOZZINI, V., TRYLSKA, J., CHANG, C.-E. & MCCAMMON, J. A. (2007). Flap opening dynamics in HIV-1 protease explored with a coarse-grained model. J. Struct. Biol. 157, 606-615.
-
(2007)
J. Struct. Biol.
, vol.157
, pp. 606-615
-
-
Tozzini, V.1
Trylska, J.2
Chang, C.-E.3
McCammon, J.A.4
-
81
-
-
34250380707
-
HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics
-
DOI 10.1529/biophysj.106.100560
-
TRYLSKA, J., TOZZINI, V., CHANG, C.-E. & MCCAMMON, J. A. (2007). HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics. Biophys. J. 92, 4179-4187. (Pubitemid 46910534)
-
(2007)
Biophysical Journal
, vol.92
, Issue.12
, pp. 4179-4187
-
-
Trylska, J.1
Tozzini, V.2
Chang, C.-E.A.3
McCammon, J.A.4
-
82
-
-
24144478280
-
Exploring global motions and correlations in the ribosome
-
DOI 10.1529/biophysj.104.058495
-
TRYLSKA, J., TOZZINI, V. & MCCAMMON, J. A. (2005). Exploring global motions and correlations in the ribo-some. Biophys. J. 89, 1455-1463. (Pubitemid 41233505)
-
(2005)
Biophysical Journal
, vol.89
, Issue.3
, pp. 1455-1463
-
-
Trylska, J.1
Tozzini, V.2
McCammon, J.A.3
-
83
-
-
0001016372
-
A comparison of techniques for calculating protein essential dynamics
-
VAN AALTEN, D.M.F., DE GROOT, B.L., FINDLAY, J. B. C., BERENDSEN, H. J. C. & AMADEI, A. (1997). A comparison of techniques for calculating protein essential dynamics. J. Comput. Chem. 18, 169-181. (Pubitemid 127598563)
-
(1997)
Journal of Computational Chemistry
, vol.18
, Issue.2
, pp. 169-181
-
-
Van Aalten, D.M.F.1
De Groot, B.L.2
Findlay, J.B.C.3
Berendsen, H.J.C.4
Amadei, A.5
-
85
-
-
44449099745
-
Coarse-grained force field for the nucleosome from self-consistent multiscaling
-
DOI 10.1002/jcc.20902
-
VOLTZ, K., TRYLSKA, J., TOZZINI, V., KURKAL-SIEBERT, V., LANGOWSKI, J. & SMITH, J. (2008). Coarse-grained force field for the nucleosome from self-consistent multi-scaling. J. Comput. Chem. 29, 1429-1439. (Pubitemid 351757766)
-
(2008)
Journal of Computational Chemistry
, vol.29
, Issue.9
, pp. 1429-1439
-
-
Voltz, K.1
Trylska, J.2
Tozzini, V.3
Kurkal-Siebert, V.4
Langowski, J.5
Smith, J.6
-
86
-
-
62349083556
-
Effective force coarse-graining
-
WANG, Y., NOID, W. G., LIU, P. & VOTH, G. A. (2009). Effective force coarse-graining. Phys. Chem. Chem. Phys. 11, 2002-2015.
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 2002-2015
-
-
Wang, Y.1
Noid, W.G.2
Liu, P.3
Voth, G.A.4
-
87
-
-
34250829219
-
OPUS-Ca: A knowledge-based potential function requiring only Cα positions
-
DOI 10.1110/ps.072796107
-
WU, Y., LU, M., CHEN, M., LI, J. & MA, J. (2007). OPUS-Ca: a knowledge-based potential function requiring only Ca positions. Protein Sci. 16, 1449-1463. (Pubitemid 46984879)
-
(2007)
Protein Science
, vol.16
, Issue.7
, pp. 1449-1463
-
-
Wu, Y.1
Lu, M.2
Chen, M.3
Li, J.4
Ma, J.5
-
88
-
-
38549133951
-
A coarse-grained α-carbon protein model with anisotropic hydrogen-bonding
-
DOI 10.1002/prot.21515
-
YAP, E.-H., FAWZI, N. L., & HEAD-GORDON, T. (2008). A coarse-grained a-carbon protein model with anisotropic hydrogen-bonding. Proteins 70, 626-638. (Pubitemid 351161925)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.70
, Issue.3
, pp. 626-638
-
-
Yap, E.-H.1
Fawzi, N.L.2
Head-Gordon, T.3
-
89
-
-
0038583687
-
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
-
DOI 10.1110/ps.0239303
-
ZACHARIAS, M. (2003). Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci. 12, 1271-1282. (Pubitemid 36597514)
-
(2003)
Protein Science
, vol.12
, Issue.6
, pp. 1271-1282
-
-
Zacharias, M.1
-
90
-
-
0036838311
-
Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction
-
DOI 10.1110/ps.0217002
-
ZHOU, H. & ZHOU, Y. (2002). Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci. 11, 2714-2726. (Pubitemid 35191145)
-
(2002)
Protein Science
, vol.11
, Issue.11
, pp. 2714-2726
-
-
Zhou, H.1
Zhou, Y.2
-
91
-
-
34247852583
-
Coarse-grained peptide modeling using a systematic multiscale approach
-
DOI 10.1529/biophysj.106.094425
-
ZHOU, J., THORPE, I. F., IZVEKOV, S. & VOTH, G. A. (2007). Coarse-grained peptide modeling using a systematic multiscale approach. Biophys. J. 92, 4289-4303. (Pubitemid 46910544)
-
(2007)
Biophysical Journal
, vol.92
, Issue.12
, pp. 4289-4303
-
-
Zhou, J.1
Thorpe, I.F.2
Izvekov, S.3
Voth, G.A.4
|